Topic 1.1 & 1.2

All living organisms are composed of cells. Multicellular organisms (example: humans) are composed of many cells while unicellular organisms (example: bacteria) are composed of only one cell. Cells are the basic unit of structure in all organisms.

Cells are the smallest unit of life. They are the smallest structures capable of surviving on their own.

Cells come from preexisting cells and cannot be created from nonliving material. For example, new cells arise from cell division and a zygote (the very first cell formed when an organism is produced) arises from the fusion of an egg cell and a sperm cell.

Metabolism - the web of all enzymes-catalyzed reactions in a cell or organism (respiration)

Response - living things can respond to and interact with the environment

Homeostasis - the maintenance and regulation of internal cell conditions (temperature, water, etc.)

Growth - living things can grow or change size/shape

Reproduction - living things produce offspring either sexually or asexually

Excretion - the removal of metabolic waste

Nutrition - feeding by either the synthesis of organic molecules (photosynthesis) or absorption of organic molecules

Cells need to produce chemical energy (via metabolism) to survive and this requires the exchange of materials with the environment

The rate of metabolism of a cell is a function of its mass / volume (larger cells need more energy to sustain essential functions)

The rate of material exchange is a function of its surface area (large membrane surface equates to more material movement). The greater the SA/volume ratio is, the faster the cell can remove waste and heat, and absorb oxygen and nutrients essential for the cell to function properly.

As a cell grows, volume increases faster than surface area, leading to a decreased SA: Vol ratio

If metabolic rate exceeds the rate of exchange of vital materials and wastes (low SA: Vol ratio), the cell will eventually die

Hence growing cells tend to divide and remain small in order to maintain a high SA: Vol ratio suitable for survival

Cells and tissues that are specialized for gas or material exchanges will increase their surface area to optimize material transfer

Living things have different levels of organization. Smaller parts combine to make increasingly complex systems. An emergent property is a characteristic an entity gains when it becomes part of a bigger system. Emergent properties help living organisms better adapt to their environments and increase their chances of survival.

Emergence in science and system theories is defined as how complex systems and patterns arise out of a multiplicity of relatively simple interactions. Basically, complex life systems involve millions of small simple interactions that work together to allow the complex system to function properly.

The emergence properties arise from the interaction of components. The whole is greater than the sum of its parts. Multicellular organisms are capability of completing functions that individual cells cannot

In multicellular organisms:

Cells may be grouped together to form tissues

Organs are then formed from the functional grouping of multiple tissues

Organs that interact may form organ systems capable of carrying out specific body functions

Organ systems collectively carry out the life functions of the complete organism

Every cell in a multicellular organism contains all genes of that organism. However, not all of those genes are activated in every cell or at the same time. When the gene is activated, the gene will encode for specific proteins. These proteins will affect the structure and function of cells.

By activating certain genes and not others, the cells are able to differentiate and form specialized tissues. Differentiation depends on gene expression which is regulated mostly during transcription. It is an advantage for multicellular organisms as cells can differentiate to be more efficient unlike unicellular organisms who have to carry out all of the functions within one cell.

In development after the zygote divides to form the blastocyst (around 120-130 cells), and then the gastrula, which is differentiated into several dermal layers of cells (mesoderm, endoderm, ectoderm, and germ cells) that form into specific specialized cells.

Differentiation is the process during development whereby newly formed cells become more specialized and distinct from one another as they mature. All cells of an organism share an identical genome – each cell contains the entire set of genetic instructions for that organism. The activation of genes within a given cell by chemical signals will cause it to differentiate.

Within the nucleus of a eukaryotic cell, DNA is packaged with proteins to form chromatin. Active genes are usually packaged in an expanded form called euchromatin that is accessible to transcriptional machinery. Inactive genes are typically packaged in a more condensed form called heterochromatin (saves space, not transcribed). Differentiated cells will have different regions of DNA packaged as euchromatin and heterochromatin according to their specific function

Stem cells are cells that are not fully differentiated but have the ability to divide and differentiate into different types of cells (e.g. one stem cell can differentiate into a blood cell, a liver cell or a kidney cell). Stem cells are necessary in embryonic development as all the cells in the adult organism stem from the embryonic stem cells.

Stem cells can divide many times and into many types of cells. Early stage embryos are made up of stem cells that make up all future cells. As the embryonic cells divide they gradually become committed and therefore are no longer stem cells. Some stem cells remain in the adult organism (e.g. bone marrow, skin and liver). These adult stem cells are pluripotent but not totipotent (i.e. can differentiate into many different cells but not all types of cells). Adult stem cells are vital for repair and regeneration of damaged tissue. Stem cells are ideal for therapeutic use in tissue repair and degenerative diseases

When a cell differentiates and becomes specialized, it loses its capacity to form alternative cell types

Stem cells are unspecified cells that have two key qualities:

Self-Renewal – They can continuously divide and replicate

Potency – They have the capacity to differentiate into specialized cell types

There are four main types of stem cells present at various stages of human development:

Totipotent – Can form any cell type, as well as extra-embryonic (placental) tissue (e.g. zygote)

Pluripotent – Can form any cell type (e.g. embryonic stem cells)

Multipotent – Can differentiate into a number of closely related cell types (e.g. hematopoietic adult stem cells)

Unipotent – Cannot differentiate, but are capable of self- renewal (e.g. progenitor cells, muscle stem cells

Atypical examples of exceptions to Cell Theory

Striated muscle fibers:

Muscle cells fuse to form fibers that may be very long (>300mm)

Consequently, they have multiple nuclei despite being surrounded by a single, continuous plasma membrane

Challenges the idea that cells always function as autonomous units

Aseptate fungal hyphae:

Fungi may have filamentous structures called hyphae, which are separated into cells by internal walls called septa

Some fungi are not partitioned by septa and hence have a continuous cytoplasm along the length of the hyphae

Challenges the idea that living structures are composed of discrete cells

Giant Algae

Certain species of unicellular algae may grow to very large sizes (e.g. Acetabularia may exceed 7 cm in length)

Challenges the idea that larger organisms are always made of many microscopic cells

Other exceptions to the rule

Virus don't reproduce

Red blood cells have no nucleus

Mitochondria reproduce inside cell

Examples of Stem Cell Therapy

1. Stargardt’s Disease

An inherited form of juvenile macular degeneration that causes progressive vision loss to the point of blindness. This is caused by a gene mutation that impairs energy transport in retinal photoreceptor cells, causing them to degenerate

The disease is treated by replacing dead cells in the retina with functioning ones derived from stem cells.

2. Parkinson’s Disease

A degenerative disorder of the central nervous system caused by the death of dopamine-secreting cells in the mid-brain. Dopamine is a neurotransmitter responsible for transmitting signals involved in the production of smooth, purposeful movements. Individuals with Parkinson’s disease typically exhibit tremors, rigidity, slowness of movement and postural instability. Treatment is by replacing dead nerve cells with living, dopamine-producing ones.

3. Other Therapeutic Examples

Leukemia: Bone marrow transplants for cancer patients who are immunocompromised as a result of chemotherapy

Paraplegia: Repair damage caused by spinal injuries to enable paralyzed victims to regain movement

Diabetes: Replace non-functioning islet cells with those capable of producing insulin in type I diabetics

Burn victims: Graft new skin cells to replace damaged tissue

Stem cells can be derived from one of three sources:

Embryonic stem cells – fertilize egg with sperm, fusion forms a zygote, the cell will now divide by mitosis till it is about 12-16 cells. These are all embryonic stem cells. They can differentiate into any cell type but have a higher risk of becoming tumor cells. There is also less chance that the cells have genetic damage as they are very new and don’t have time to accumulate mutations like adult stem cells.

Umbilical Cord Stem Cells – stem cells obtained from the cord, can be frozen and used later on in life. These are easily obtained and stored after birth.

Adult Stem Cells – obtained from some adult tissue such as bone marrow. They are difficult to obtain and have less growth potential and limited capacity to differentiate when compared to embryonic stem cells; however, they are fully compatible with adult’s tissue (no rejection) and there is less chance for a malignant tumor to occur

Microscopes are scientific instruments that are used to observe objects that are too small to see with the naked eye

There are two main types of microscope: optical (light) microscopes and electron microscopes

Light Microscopes

Use lenses to bend light and magnify images by a factor of roughly 100-fold

Can be used to view living specimens in natural color

Chemical dyes and fluorescent labeling may be applied to resolve specific structures

Electron Microscopes

The electron microscope is a type of microscope that uses a beam of electrons to create an image of the specimen. It is capable of much higher magnifications and has a greater resolving power than a light microscope, allowing it to see much smaller objects in finer detail. They are large, expensive pieces of equipment, generally standing alone in a small, specially designed room and requiring trained personnel to operate them.

Use electromagnets to focus electrons resulting in significantly greater magnifications and resolutions

Can be used to view dead specimens in monochrome (although false color rendering may be applied)

Transmission electron microscopes (TEM) pass electrons through specimen to generate a cross-section

Scanning electron microscopes (SEM) scatter electrons over a surface to differentiate depth and map in 3D

To calculate the linear magnification of a drawing or image, the following equation should be used:

Magnification = Image size (with ruler) ÷ Actual size (according to scale bar)

Calculation of Actual Size:

To calculate the actual size of a magnified specimen, the equation is simply rearranged:

Actual Size = Image size (with ruler) ÷ Magnification

Relative Sizes of Biological Materials

Eukaryotic cell (plant) = ~100 μm

Eukaryotic cell (animal) = ~10 – 50 μm

Organelle (e.g. mitochondrion) = ~1 – 10 μm

Prokaryotic cell (bacteria) = ~1 – 5 μm

Virus = ~100 nm

Plasma membrane = ~7.5 nm

Molecules (e.g. glucose) = ~1 nm

Atoms = ~100 pm

Cells and their components are measured according to the metric system

Prokaryotes are organisms whose cells lack a nucleus ('pro' = before; 'karyon' = nucleus)

They belong to the kingdom Monera and have been further classified into two distinct domains:

Archaebacteria – found in extreme environments like high temperatures, salt concentrations or pH (i.e. extremophiles)

Eubacteria – traditional bacteria including most known pathogenic forms (e.g. E. coli, S. aureus, etc.)

Features of Prokaryotes

Cell wall – rigid outer covering made of peptidoglycan; maintains shape and prevents bursting (lysis)

Slime capsule – a thick polysaccharide layer used for protection against desiccation (drying out) and phagocytosis

Flagella – Long, slender projections containing a motor protein that enables movement (singular: flagellum)

Pili – Hair-like extensions that enable adherence to surfaces (attachment pili) or mediate bacterial conjugation (sex pili)

Cell membrane – Semi-permeable and selective barrier surrounding the cell

Cytoplasm – internal fluid component of the cell

Nucleoid – region of the cytoplasm where the DNA is located (DNA strand is circular and called a genophore)

Plasmids – autonomous circular DNA molecules that may be transferred between bacteria (horizontal gene transfer)

Ribosomes – complexes of RNA and protein that are responsible for polypeptide synthesis (prokaryote ribosome = 70S)

Eukaryotes are organisms whose cells contain a nucleus (‘eu’ = good / true; ‘karyon’ = nucleus)

They have a more complex structure and are believed to have evolved from prokaryotic cells (via endosymbiosis)

Prokaryotic cells are fundamentally different in their internal organization from eukaryotic cells. Notably, prokaryotic cells lack a nucleus and membranous organelles. The nucleus is bounded by the nuclear envelope, a double membrane with many nuclear pores through which material enters and leaves.

Prokaryotic cells divide by binary fission. This involves the replication of their DNA and elongation of the cell such to the point that it will partition or divide into two cells. ... Binary fission is a form of asexual reproduction and this means that the two cells produced are genetically identical to the original cell.

Eukaryotes can be divided into four distinct kingdoms:

Protista – unicellular organisms; or multicellular organisms without specialized tissue

Fungi – have a cell wall made of chitin and obtain nutrition via heterotrophic absorption

Plantae – have a cell wall made of cellulose and obtain nutrition autotrophically (via photosynthesis)

Animalia – no cell wall and obtain nutrition via heterotrophic ingestion

Universal Organelles

Ribosomes - these organelles consist of RNA and proteins and are responsible for protein production. Ribosomes are found suspended in the cytosol or bound to the endoplasmic reticulum.

Cytoskeleton - these structures are filamentous scaffolding within the cytoplasm (fluid portion of the cytoplasm is the cytosol). The cytoskeleton provides internal structure and mediates intracellular transport (less developed in prokaryotes)

Plasma membrane - this is a phospholipid bilayer embedded with proteins (not an organelle, but a vital structure). The plasma membrane is a semi-permeable and selective barrier surrounding the cell

Organelles of Eukaryotes

Nucleus - a membrane bound structure that contains the cell's hereditary (DNA) information and controls the cell's growth and reproduction. It is commonly the most prominent organelle in the cell.

Mitochondria - as the cell's power producers, mitochondria convert energy into forms that are usable by the cell. They are the sites of cellular respiration which ultimately generates fuel for the cell's activities. Mitochondria are also involved in other cell processes such as cell division and growth, as well as cell death.

Endoplasmic Reticulum - extensive network of membranes composed of both regions with ribosomes (rough ER) and regions without ribosomes (smooth ER). This organelle manufactures membranes, secretory proteins, carbohydrates, lipids, and hormones.

Golgi complex - also called the Golgi apparatus, this structure is responsible for manufacturing, warehousing, and shipping certain cellular products, particularly those from the endoplasmic reticulum (ER).

Peroxisomes - Like lysosomes, peroxisomes are bound by a membrane and contain enzymes. Peroxisomes help to detoxify alcohol, form bile acid, and break down fats.

Vacuole - these fluid-filled, enclosed structures are found most commonly in plant cells and fungi. Vacuoles are responsible for a wide variety of important functions in a cell including nutrient storage, detoxification, and waste exportation.

Centrioles - these cylindrical structures are found in animal cells, but not plant cells. Centrioles help to organize the assembly of microtubules during cell division.

Cilia and Flagella - cilia and flagella are protrusions from some cells that aid in cellular locomotion. They are formed from specialized groupings of microtubules called basal bodies

Animals Only

Lysosome - membranous sacs filled with hydrolytic enzymes that will breakdown / hydrolysis of macromolecules (presence in plant cells is unsure)

Plants Only

Chloroplast - this chlorophyll containing plastid is found in plant cells, but not animal cells. Chloroplasts absorb the sun's light energy for photosynthesis.

Cell Wall - this rigid outer wall is positioned next to the cell membrane in most plant cells. Not found in animal cells, the cell wall helps to provide support and protection for the cell.